Vivaria house a number of animals, typically test animals, such as mice, in a number of cages, often a large number. The test animals are frequently used to test drugs, genetics, animal strains, husbandry experiments, methods of treatment, procedures, diagnostics, and the like. We refer to all such uses of a vivarium as a study.
The animals in a vivarium must be observed, either manually by humans or by automated means, such as by the use of video cameras and video analytics software. Comparisons of animals are the basis of any study result.
There are a large number of animal characteristics, attributes, or behavior that may be of interest in a study. We refer to all such observable aspects of animals as “behaviors,” including blood, saliva, feces, urine, breath, and fur attributes. Observations of behaviors may be manual or automated and may be invasive or non-invasive. They may occur in the animal's home cage; or in a separate observation or test cage or apparatus; or via pathology or other chemical, biological or analytical analysis. Observations and results may use statistics or aggregated behaviors.
For observing all such behaviors, it is critical that the observed behaviors be reliably, easily, and quickly linked to one particular animal. It is also necessary that marking the animals be consistent, fast, reliable and low cost. It is also necessary that reading the animal ID be highly reliable, fast, and low cost. Not only is it necessary that reading be reliable, but also necessary that the actual reliability is measurable. It is desirable that reading algorithms are adjustable such that higher reliability may be traded off against more “non reads.” It is also desirable that the size of a code space used may be traded off against readability.
Prior art uses a variety of animal identification systems, including one animal per cage, ear notches, ear tags, foot and toe pad tattooing, embedded RFID, attached RFID, body tattoos, and tail tattoos. Some prior art uses human-readable markings, such as ear notches or ID numbers tattooed on a tail. Some prior art uses machine-readable markings, such as RFIDs, ear-tag barcodes, and tail barcodes.
In an ideal world, each animal might receive a globally unique ID that is never re-used. However, that requires a large code space, which in return requires complex markings. Small animal tails are a poor choice substrate for placing readable codes. complex codes either cannot be marked at all, or do not read reliably. In prior art practice, markings are often in a very small code space and other systems are used to uniquely identify an animal. One such prior art method is a marking that is unique only within a single cage. For example, colored ear tags may be used, with only five colors available. Alternatively, ear notches may be used providing a code space size of less than 100. Another prior art method uses unique markings within a single study. Animals in one study are generally kept well apart from animals in another study; thus, unique marking within one study may be sufficient.
All such prior art has significant weaknesses. For machine-readable markings weaknesses include:                risk of confusing one animal with another, for example, if an animal is moved to a wrong cage        not human-readable        slow reading        requires specialized equipment        expensive equipment and expensive to read        computer required to read and map animal ID        may have single-vendor lock-in        two hands often required to use equipment        accuracy and reliability may not be computable or traceable        slow and expensive to mark animals        limited through rate for marking new animals        animals may have to be a minimum age to mark        may work only in-cage or may work only out-of-cage        either applying marks or reading marks may not be sterile        animal may have to anesthetized to be marked.        
For human-readable markings weaknesses include:                risk of confusing one animal with another, for example, if an animal is moved to a wrong cage        often not machine-readable        may not be readable in the dark—the animals' natural activity period        reading may be unreliable        typically has a small code space        requires manual data entry to link animal ID to stored data        likely not suitable for machine marking        high labor cost for marking        accuracy and reliability may not be computable or traceable        limited through rate for marking new animals        slow through rate for marking new animals.        
Embodiments of this invention overcome many of the weaknesses of prior art.